BIO120 - Evolution

Key concepts and vocabulary

Genotype

genetic composition of an organism, in relation to a particular gene e.g. Aa, AaBB

Phenotype

observable characteristic, e.g. colour of fur, shape of teeth, enzyme activity, mRNA expression —> regulates genes —> can be observed

Genome

all of the organisms nuclear DNA, not organelle DNA

Describe the three key points of Darwin’s mechanism of natural selection

Population must experience VARIATION, the trait is HERITABLE, some traits allow the organisms to be more successful at surviving/reproducing (FITNESS)

What are the sources of variation

Mutation, recombination, independent assortment, genetic drift, natural selection, gene flow (migration)

Mutation

an inevitable, and permanent error in DNA replication; can be beneficial, harmful, natural

Characteristics of mutation and what effect it tends to have on diversity

• isn’t directed towards a specific outcome/no specific purpose

• inevitable in all living organisms

• rate depends on type of mutation

• tends to INCREASE diversity

What are the different types of mutations? Give examples

1. Point mutation ie, AGTTC —> AGATC

2. Indels

   1. Insertion ie. AGTTC —> AGTAGCTC

   2. Deletion ie. AGTTCATG —> AGTTG

3. Changes in repeat number ie. ATGATGATG —> ATGATGATGATG

4. Inversions (Chromosomal rearrangements) ie. ATGCAGT —> TGACGTA

Do all mutations cause some sort of harm/alter the genome?

No, silent mutations can occur when the change in one amino acid still codes for the same enzyme. These are very common

ie. TTT (phenylalanine) —> TTC (phenylalanine

Describe Independent assortment

2 diploid chromosomes in each parent undergo meiosis and produces 4 haploid gametes with random combinations of paternal and maternal chromosomes

RESULT:

4 gamete combos from one parent, 4 gamete combos from another parent

—> creates 16 different combinations of offspring

Characteristic + math of independent assortment

• allows for different combinations of parental chromosomes (exponential: 2^x where x = # of pairs of chromosomes)

Describe recombination and what effect it has on diversity

• occurs during Meiosis

• when sister chromatids within the homologous chromosome pair cross over at chiasmata (point where chromosomes touch)

• chromosome of mom as a bit of dad, chromosome of dad has a bit of mom

• tends to INCREASE diversity

Describe the theory of heredity before Mendel and WHY it was wrong.

Theory of blending inheritance; characteristics from both parents mixed together permanently

Wrong bc it leaves no room for variations to increase in frequency, they become diluted until practically gone

ie. blue + yellow = green // next gen // green + yellow = greeny // blue is completely gone

What did Mendel find in his pea experiment that questioned blending inheritance?

Traits were able to be preserved into next generations even if they didn’t show up in the previous

Describe Mendel’s findings from his pea experiment

1. inheritance is determined by genes

2. each diploid organism carries two copies of (alleles) of each gene

   1. alleles can exhibit dominance or recessivity

   2. gametes produced only contain one allele per gene (per characteristic)

3. gametes fuse to make offspring (sperm + egg fuse)

4. offspring randomly inherit one allele per gene from each parent

Compare simple “Mendelian” genetics to complex inheritance

Mendelian genetics are described to behave discretely, with traits being one or the other

Complex inheritance are continuous, traits can come in a wide range ie. height

How does discrete trait inheritance become continuous?

Beginning with two discrete genotypes (aa, AA) —> partial dominance allows there to be an “inbetween (Aa) —> adding a locus (B or b) allows more variation and creates more “inbetweens” (Aabb, AABb) which slowly develops into continuous inheritance

What evidence is there for evolution

Geology, Homolgy, Biogeography, Domestication

What did we learn about geology in terms of evolution?

• Earth is very old, allowed for immense time for evolution

• Evidence of transitional fossils that link features of completely diff species

• Younger fossils resembled modern species in the same region

What did homology tell us about evolution?

• Vestigial structures provide evidence of evolutionary past

  • traits ancestors used that have lost significance over time

• Homologous structures are found everywhere across organisms

  • all descended from common ancestor

  • these structures evolved to serve different functions depending on organism

What did we learn from biogeography?

• isolated regions cause species to have unique adaptations for their environment

What evidence of evolution do we have from domestication?

• organisms have variations that are heritable and can be selected to lead to desirable traits

What did Darwin’s findings help us discover in more modern times?

• antibiotic resistance, herbicide resistance, adaptation to pollution

• discovery of molecular evolution

• fossils have furthered our knowledge of past life and transitional forms

Describe who was responsible for ideas of biology before Darwin and Wallace

1. Paley’s argument from design:

Natural theology suggests attributes are designed (by God) and serve a certain purpose

2. Lamarck’s inheritance of acquired characteristics:

organisms develop traits in their lifetime that increase their fitness and are passed down to next generations

Why was Lamarck wrong? Who proved him wrong?

Weissmann’s germplasm theory:

Inheritance is only through germ cells (gametes), somatic cells (body) don’t contribute to heredity

What were the two major theses of Darwin and Wallace’s theory of evolution

1. all organisms descended from a common ancestor

2. process the leads to evolution is natural selection among varying individuals

What influenced Darwin’s reasoning for the theory of evolution and how?

Lyell’s principles of geology:

idea of uniformitarianism - forces that shape earth are constant over time, present day geology reflects that of the past

• Darwin: the world must be changing, those mechanisms for change are the same now vs. before

Malthus’ essay on the principle of population:

The population will continue to grow exponentially, there is a competition for resources

• Darwin: favourable variations would be preserved, unfavourable destroyed

List the 4 important elements of Darwin’s theory

1. evolution occurs in the level of populations, individuals don’t evolve

2. individuals don’t create variation when needed

3. fitness depends on the environment

4. evolution works with available variation, doesn’t create from scratch

Evolutionary history vs. Evolutionary mechanisms

History: studying diversification of life over the years, how lineages diverged to create speciation

Mechanisms: how these changes that caused divergence arose

Microevolution vs. Macroevolution

Micro: evolutionary patterns + process within a species

Macro: evolutionary patterns + process among species

What are the goals and ways to practice evolutionary history?

Goal: determine evolutionary relationships in terms of a common ancestor, identify patterns in evolution

Practice: comparative data from biogeography, paleontology, etc.

Describe how phylogenetic trees work

branches representing lineages and nodes representing common ancestors and speciation events

What are the goals and ways to practice evolutionary mechanisms

Goals: determine processes responsible for evolutionary change

Practice: use experimental, theoretical, comparative studies of genetics on a population level

List 4 ways evolution can be studied, provide examples

Observational: describe and quantify, go touch grass

Theoretical: create models, verbal graphical, mathematical etc.

Comparative: get same data from diff species, “is sth in one group also true in the other?”

Experimental: manipulate system to address hypothesis

Describe genetic drift and what effect it tends to have on diversity.

• change in frequency of a gene from random chance

• larger effect on smaller populations

• tends to DECREASE genetic variation (net effect over a long time)

Describe gene flow and what effect it has on diversity

• when population migrates to another location and reproduce, spread genetic material

• both populations become more similar

• INCREASE in diversity

Describe natural selection and its types as well as the effect it has on diversity

• Negative selection (purifying) remove mutations that reduce fitness —> DECREASE diversity

• Positive selection (directional/adaptation) favour mutations that increase fitness, eventually become FIXED population —> DECREASE diversity

• Selection favouring diversity maintain diversity over a long time (heterozygote advantage ie. Aa over AA) —> INCREASE diversity

What is heterozygote advantage, give an example

when a chromosome contains two different alleles for a gene which increases fitness of the organism

ie. ppl heterozygote for sickle cell gene are also resistant to malaria vs. sickle cell anemia in homozygous ppl.

What are ways we can quantify genetic variation?

Heterozygosity and polymorphism

Describe how we quantify genetic variation using heterozygosity

number of heterozygous individuals / total individuals in a locus

ie. H = 2 heterozygous ppl / 5 total ppl = 0.4 (40%)

Describe how we quantify genetic variation using polymorphism

number of polymorphic loci (two or more alleles) / total number of loci

ie. P = 3 polymorphic genes / 4 total loci = 0.75 (75%)

If two alleles code for the same gene, how is heterozygote advantage possible?

two alleles code for the same gene but can produce different forms of proteins

ie. HbA allele = normal blood cell, HbS allele = sickle cell

homozygous individuals would either have normal blood cells and be susceptible to malaria, or have sickle cell anemia which can be fatal

heterozygous individuals have some HbA and HbS, so not fatal sickle cell disease while also being more resistant to malaria (best of both worlds!)

What is polymorphism

A polymorphic gene is a gene where two or more alleles occur at the same locus (location) on the DNA across a population, and each of these alleles appears at a frequency of at least 1%.

Describe the classical school model for population genetic variation and who was mainly responsible for it.

1. Classical school (Morgan, Muller)

   • mutations reintroduce less fit traits by random

     • selection activity removes the less fit ones

   • variation eliminated —> will be one “best/ideal” allele

   • low heterozygosity

   • low polymorphism

Describe the balance school model for population genetic variation and who was mainly responsible for it.

2. Balance school (Dobzhansky, Ford)

   • heterozygote individuals have higher advantage —> high heterozygosity

   • high polymorphism

   • both of the heterozygote alleles persist —> favour diversity

   • fitness depends on variation of the allele

     • rare alleles are less likely to be selected upon and being eliminated (unless genetic drift)

What technology was used to provide insight on what proportion of genes show genetic variation (polymorphic & heterozygosity)

Allozyme gel electrophoresis:

• blend up sample and extract the protein

• put into gel and send electrical current

• DNA is slightly negative —> will move towards positive charged end

• can see how many alleles in the sampl,

Describe how high polymorphism correlates to high heterozygosity

if a locus has multiple alleles that are fairly balanced in frequency, the chance that an individual carries two different alleles is high (high poly —> high hetero)

Describe the branch of reproductive models (6 terms total)

Asexual, Sexual

Sexual —> Dioecious, Hermaphrodite

Hermaphrodite —> Cross-fertilization, Self-fertilization 

Describe the 2 types of asexual reproduction

Parthenogenesis - embryo develops from the egg but no fertilization

Clonal propagation - no egg

Describe sexual reproduction

• 2 parents contribute genetic material to the offspring

• meiosis, haploid —> diploid

• fusion of gametes

Describe asexual reproduction

• 1 parent contributes genetic material

• no meiotic reductive devision

• offspring are clones

Describe the costs of sexual reproduction

1. Two-fold Cost

• female leaves behind half as many genes

  • contributes 4 genes for 4 offspring but asexual contribute 8 for 4 offspring

2. Breaks up favourable combinations of Alleles

• If the heterozygote has low fitness, reproduction of a homozygous + homozygous will always result in half being heterozygous

3. Can take a lot of time and energy to attract mates, reproduce

4. Risk of predation & infection

Describe the benefits of sexual

1. Favourable mutations brought together more rapidly

• asexual doesn’t allow crossing, favourable traits can only pop up through the right mutation

2. Can eliminate harmful mutations (picture shown)

3. high variability = likely to do well in unpredictable world

• Tangled Bank hypothesis

  • offspring may encounter diff environments, better to hedge bets of survival w/ variation

• Red Queen hypothesis

  • species must constantly adapt and evolve to conditions that change constantly

What asexual reproduction disadvantages were discovered with the experiment involving the Oenothera flowers

1. asexual Oenothera had “premature'“ stop codons, cause dysfunctional proteins

2. higher rates of protein sequence evolution —> more mutations —> no way to purge them out

3. increased accumulation of harmful mutations

Define the terms outbreeding, inbreeding, outcrossing, and self-fertilization

Outbreeding: mates are less closely related

Inbreeding: mates are more closely related

Outcrossing: mating with someone else, fusion of 2 gametes (usually used in context for hermaphrodites)

Selfing: mating with yourself, fusion of 1 gamete (usually used in context for hermaphrodites)

What is the difference between self-fertilization and asexual reproduction?

Self-fertilization doesn’t yield clones, still exchange of gametes b/w male and female parts

What factors lead to inbreeding?

1. local population subculture increases interests in mating among relatives

2. small population

3. hermaphroditic organisms that’s self-fertilize

What changes on a genetic level happen as a result of inbreeding?

• increased homozygosity

• decreased heterozygosity

• no direct change in allele frequencies/polymorphism

What is inbreeding depression

• inbreeding can lead to inbreeding depression if offspring have reduced fitness

• can cause abnormal phenotypes

• can change polymorphism

Why can inbreeding reduce fitness?

Homozygous recessive bad alleles are hidden (bc recessive) until the organism loses all heterozygosity which can cause weird phenotypes

Describe some mechanisms in flowering plants and animals that help to avoid inbreeding

Flowering Plants

1. physical separation, wrong position of anthers and stigma in the same flower

2. self-recognition where stigma and detect its own pollen and reject

Animals

1. dispersal, one sex will leave its family group when mature to avoid mating with relatives

2. can recognize relatives through smell, visuals

3. siblings will mature and reproduce at different times

If inbreeding is so bad, why does plants continue to self-fertilize?

selfing produces more copies of the genes, has transmission advantage (goal of plants is to spread seeds and rule the world)

Describe selective advantage

the amount a given genotype is better adapted to the environment

What are the three types of selection on quantitative traits?

1. Stabilizing

• Favours the mean, average trait increases in frequency, selected against the extremes

  • infant mortality rate in relation to birth weight

1. Directional

• Favours one extreme, shifts the whole distribution towards on of the extremes

  • Galapagod finches developed deeper beaks to break harder seeds

1. Disruptive

• Favours both extremes, average traits decrease in frequency

  • African finches adapted for soft seeds and hard seeds

What is a hitchhiker allele? Is it beneficial or detrimental?

A hitchhiker allele is one that is physically close to a beneficial allele on DNA, when the beneficial allele increases in frequency, the hitchhiking allele will be inherited as well 

What is a selective sweet

Selection causes new mutation to icrease in frequency so quickly that "hitchhikers” also increase in frequence